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Sample GSM380729 Query DataSets for GSM380729
Status Public on Jul 15, 2009
Title CIS_665PMS
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics disease state: CIS
cell type: Peripheral blood mononuclear cells
age: 36
gender: Female
time to next relapse(days): NoRelapse
Treatment protocol Peripheral blood mononuclear cells (PBMC) were separated on ficoll-hypaque gradient
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA)
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA
 
Hybridization protocol cDNA was synthesized, labeled, hybridized to either HU-133A or HU133A-2 containing 22,215 gene-transcripts according to Affymetrix (Inc, Santa Clara, CA) protocol
Scan protocol Hewlett Packard, GeneArray-TM scanner G2500A
Description working set14
Data processing Data analysis was performed by Partek Genomics Solution software (www.partek.com ). Expression values were computed from raw CEL files by applying the Robust Multi-Chip Average (RMA) background correction algorithm. The RMA correction included: 1) values background correction; 2) quantile normalization; 3) log2 transformation; 4) median polish summarization. In order to avoid the noise caused by variable set effects we normalized each set to pre-saved distribution pattern of a well balanced set used as a reference distribution. To reduce batch effect, Analysis of Variance (ANOVA) multiple model analysis was applied. Source of variation was analyzed; non-relevant batches effects such as array type, working batch, patient age and gender were eliminated.
 
Submission date Mar 16, 2009
Last update date Jul 14, 2009
Contact name Michael Gurevich
E-mail(s) Michael.Gurevich@sheba.health.gov.il
Organization name Sheba Medical Center
Department Multiple Sclerosis Center
Lab Neurogenomics and Neuroimmunology
Street address Tel Hashomer
City Ramat Gan
ZIP/Postal code 52621
Country Israel
 
Platform ID GPL96
Series (1)
GSE15245 Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
1007_s_at 6.586390018
1053_at 5.780039787
117_at 7.276850224
121_at 7.887199879
1255_g_at 3.192420006
1294_at 8.492600441
1316_at 5.199800014
1320_at 3.837640047
1405_i_at 9.816109657
1431_at 3.388180017
1438_at 5.528649807
1487_at 7.103929996
1494_f_at 5.466380119
1598_g_at 7.937469959
160020_at 6.945059776
1729_at 8.344229698
1773_at 5.348360062
177_at 4.334529877
179_at 8.397760391
1861_at 5.063189983

Total number of rows: 22215

Table truncated, full table size 494 Kbytes.




Supplementary file Size Download File type/resource
GSM380729.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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